1FMZ - JenaLib

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

Biological Unit 2

Biological Unit 3

collapse

expand

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF A MUTANT WINGED BEAN CHYMOTRYPSIN INHIBITOR PROTEIN, N14K.

Authors :   J. K. Dattagupta, C. Chakrabarti, S. Ravichandran, J. Dasgupta, S. Gho

Date :   19 Aug 00 (Deposition) - 19 Feb 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (2x)

Keywords :   Beta Trefoil, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ravichandran, J. Dasgupta, C. Chakrabarti, S. Ghosh, M. Singh, J. K. Dattagupta
The Role Of Asn14 In The Stability And Conformation Of The Reactive-Site Loop Of Winged Bean Chymotrypsin Inhibitor: Crystal Structures Of Two Point Mutants Asn14-->Lys And Asn14-->Asp.
Protein Eng. V. 14 349 2001
PubMed-ID: 11438758 | Reference-DOI: 10.1093/PROTEIN/14.5.349
(for further references see the PDB file header)

Compounds

Molecule 1 - CHYMOTRYPSIN INHIBITOR 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organ	:	SEED
	Organism Common	:	WINGED BEAN
	Organism Scientific	:	PSOPHOCARPUS TETRAGONOLOBUS
	Organism Taxid	:	3891
	Synonym	:	WCI-3

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 5)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 10)

No.	Name	Count	Type	Full Name
1	SO4	10	Ligand/Ion	SULFATE ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , SER A:128 , HOH A:206	BINDING SITE FOR RESIDUE SO4 A 900
2	AC2	SOFTWARE	HIS A:154 , ASP A:156 , ARG A:157	BINDING SITE FOR RESIDUE SO4 A 901
3	AC3	SOFTWARE	PRO A:25 , HIS A:26 , ILE A:27 , HIS A:30 , ARG A:50 , HIS A:127 , LEU A:171 , GLU A:172 , HOH A:310	BINDING SITE FOR RESIDUE SO4 A 902
4	AC4	SOFTWARE	SER A:69 , LEU A:70 , SER A:91 , TRP A:93 , HOH A:288 , HOH A:318 , HOH A:361 , HOH A:376	BINDING SITE FOR RESIDUE SO4 A 904
5	AC5	SOFTWARE	HIS A:30 , HIS A:127	BINDING SITE FOR RESIDUE SO4 A 905

SS Bonds (2, 2)

Asymmetric Unit

No.	Residues
1	A:44	-	A:88
2	A:138	-	A:147

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1FMZ)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1FMZ)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	1	A:7-23

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	1	A:7-23

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	2	A:7-23

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	ICW3_PSOTE	28-44	2	A:7-23

Exons (0, 0)

(no "Exon" information available for 1FMZ)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:179
 aligned with ICW3_PSOTE | P10822 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:179
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192         
           ICW3_PSOTE    23 TADDDLVDAEGNLVENGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQFLSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 201
               SCOP domains d1fmza_ A: chymotrypsin inhibitor WCI                                                                                                                                               SCOP domains
               CATH domains 1fmzA00 A:2-180  [code=2.80.10.50, no name defined]                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeee.hhhhh..eeee.........eeee..........eeeee............eeeee............eee......eee......hhhhh..eeeee........eeeeeeee....eeeeeeeeeee.....eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SOYBEAN_KUNITZ   ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fmz A   2 EFDDDLVDAEGNLVEKGGTYYLLPHIWAHGGGIETAKTGNEPCPLTVVRSPNEVSKGEPIRISSQFLSLFIPRGSLVALGFANPPSCAASPWWTVVDSPQGPAVKLSQQKLPEKDILVFKFEKVSHSNIHVYKLLYCQHDEEDVKCDQYIGIHRDRNGNRRLVVTEENPLELVLLKAKS 180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Trefoil (385)

Superfamily: STI-like (91)

Family: Kunitz (STI) inhibitors (29)

Protein domain: chymotrypsin inhibitor WCI (8)

Winged bean (Psophocarpus tetragonolobus) [TaxId: 3891] (8)

d1fmza_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Trefoil (289)

Topology: Trefoil (Acidic Fibroblast Growth Factor, subunit A) (289)

Homologous Superfamily: [code=2.80.10.50, no name defined] (289)

Winged bean (Psophocarpus tetragonolobus) (12)

1fmzA00

A:2-180

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1FMZ)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (ICW3_PSOTE | P10822)

molecular function
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fmz)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1fmz
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ICW3_PSOTE \| P10822
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ICW3_PSOTE \| P10822
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	ICW3_PSOTE \| P10822	:	1eyl 1fn0 1wbc 1xg6 2bea 2beb 2esu 2et2 2qyi 2wbc 3i29 3i2a 3i2x 3qyd 3veq 4h9w 4ha2 4tlp 4wbc

Related Entries Specified in the PDB File

1eyl	1EYL IS THE SAME PROTEIN IN RECOMBINANT FORM
1fn0	1FN0 CONTAINS THE SAME PROTEIN
1wbc	CRYSTAL STRUCTURE OF THE SAME PROTEIN (NATIVE) AT 2.95A RESOLUTION
2wbc	CRYSTAL STRUCTURE OF THE SAME PROTEIN (NATIVE) AT 2.3A RESOLUTION
4wbc	CRYSTAL STRUCTURE OF THE SAME PROTEIN (NATIVE) AT 2.13A RSOLUTION.